9PZW | pdb_00009pzw

GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9PZW

This is version 1.1 of the entry. See complete history

Literature

Cryo-EM of autoantibody-bound NMDA receptors reveals antigenic hotspots in an active immunization model of anti-NMDAR encephalitis.

Kim, J.Jalali-Yazdi, F.Jones, B.E.Westbrook, G.L.Gouaux, E.

(2026) Sci Adv 12: eaeb4249-eaeb4249

  • DOI: https://doi.org/10.1126/sciadv.aeb4249
  • Primary Citation Related Structures: 
    9PZQ, 9PZR, 9PZS, 9PZT, 9PZU, 9PZV, 9PZW, 9PZX

  • PubMed Abstract: 

    Autoantibodies targeting synaptic membrane proteins are associated with autoimmune encephalitis manifested by seizures, psychosis, and memory dysfunction. Anti- N -methyl-d-aspartate receptor (NMDAR) encephalitis, a prototype of these autoimmune synaptic disorders, is unexpectedly common. Unfortunately, how the native repertoire of anti-NMDAR autoantibodies recognizes NMDARs and the precise locations of antigenic epitopes remain poorly understood. Here, we used an active immunization model that closely mimics the human disease to immunize adult mice with intact GluN1/GluN2A receptors, resulting in fulminant autoimmune encephalitis. Serum was collected at 6 weeks postimmunization for single-particle cryo-electron microscopy of GluN1/GluN2A receptors complexed with purified polyclonal anti-NMDAR autoantibody fragments. Native autoantibodies recognized two distinct binding sites on the GluN1 amino-terminal domain, which we confirmed using monoclonal antibodies bound to native NMDARs purified from mouse brain. Structural analysis of autoantibody-bound NMDAR complexes identified antigenic hotspots within the GluN1 amino-terminal domain. These hotspots provide potential targets for therapeutic intervention.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health & Science University, 3232 SW Research Drive, Portland, OR 97239, USA.

Macromolecule Content 

  • Total Structure Weight: 447.93 kDa 
  • Atom Count: 27,525 
  • Modeled Residue Count: 3,493 
  • Deposited Residue Count: 3,970 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2A [auth J],
G [auth L]
141Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2B [auth K],
H [auth M]
131Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1C [auth A],
E [auth C]
847Rattus norvegicusMutation(s): 0 
Gene Names: Grin1Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus)
Explore P35439 
Go to UniProtKB:  P35439
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35439
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P35439-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2AD [auth B],
F [auth D]
866Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus)
Explore Q00959 
Go to UniProtKB:  Q00959
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00959
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q00959-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
J [auth A]
K [auth A]
L [auth A]
AA [auth D],
BA [auth D],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU
(Subject of Investigation/LOI)

Query on GLU



Download:Ideal Coordinates CCD File
N [auth B],
Z [auth D]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
GLY
(Subject of Investigation/LOI)

Query on GLY



Download:Ideal Coordinates CCD File
I [auth A],
S [auth C]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.
RECONSTRUCTIONcryoSPARC4.4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-02-04
    Changes: Data collection, Database references